|
| Status |
Public on Nov 21, 2023 |
| Title |
CEN.PK113-7D mtRNA Glucose replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Isolated mitochondria of S. cerevisiae cell culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
replicate: Replicate 3
strain: CEN.PK113-7D
carbon source: Glucose
|
| Treatment protocol |
Mitochondria were isolated from whole cells by a process of spheroplasting, homogenization and differential centrifugation
|
| Growth protocol |
Cells were grown in shake flasks containing 100 mL synthetic medium supplied with either glucose r ethanol-glycerol as carbon source, and harvested in mid-exponential phase
|
| Extracted molecule |
other |
| Extraction protocol |
RNA was extracted using the miRNeasy Mini kit (Qiagen) with on-column DNA digestion
Samples were poly(A) tailed enzymatically using using E. coli Poly(A) Polymerase (New England Biolabs #M0276), then purified using the miRNeasy Mini kit (Qiagen). Poly(A)-tailed RNA samples were used for library preparation using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies [ONT], Oxford, UK), following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
rnaseq_CPM_Glu.csv
|
| Data processing |
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts normalized with CPM from edgeR
Assembly: CEN.PK113-7D ASM257140v2
Supplementary files format and content: Comma delimited file, normalized transcript counts
|
| |
|
| Submission date |
Nov 29, 2022 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Marcel van den Broek |
| E-mail(s) |
marcel.vandenbroek@tudelft.nl
|
| Organization name |
Delft University of Technology
|
| Street address |
Van der Maasweg 9
|
| City |
Delft |
| ZIP/Postal code |
2629 HZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL25739 |
| Series (1) |
| GSE219013 |
Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN31929305 |
| SRA |
SRX18415099 |
